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Report generated at 2020-06-10 05:48:45

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	70770612	96892848
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70216364	95177950
Mapped(QC-failed)	0	0
% Mapped	99.2200	98.2300
Paired	70770612	96892848
Paired(QC-failed)	0	0
Read1	35385306	48446424
Read1(QC-failed)	0	0
Read2	35385306	48446424
Read2(QC-failed)	0	0
Properly Paired	69713731	93194227
Properly Paired(QC-failed)	0	0
% Properly Paired	98.5100	96.1800
With itself	69835807	94492205
With itself(QC-failed)	0	0
Singletons	380557	685745
Singletons(QC-failed)	0	0
% Singleton	0.5400	0.7100
Diff. Chroms	20273	166792
Diff. Chroms (QC-failed)	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

	rep1	ctl1
Unpaired Reads	0	0
Paired Reads	32882196	40925788
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	447802	246444
Paired Opt. Dupes	2496	1204
% Dupes/100	0.0136	0.0060

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	32871471	40844131
Distinct Read Pairs	32424350	40626962
One Read Pair	31990179	40418355
Two Read Pairs	422811	204968
NRF = Distinct/Total	0.9864	0.9947
PBC1 = OnePair/Distinct	0.9866	0.9949
PBC2 = OnePair/TwoPair	75.6607	197.1935

Mitochondrial reads are filtered out.

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Flagstat (filtered/deduped BAM)

Filtered and duplicates removed

	rep1	ctl1
Total	64868788	81358688
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	64868788	81358688
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	64868788	81358688
Paired(QC-failed)	0	0
Read1	32434394	40679344
Read1(QC-failed)	0	0
Read2	32434394	40679344
Read2(QC-failed)	0	0
Properly Paired	64868788	81358688
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	64868788	81358688
With itself(QC-failed)	0	0
Singletons	0	0
Singletons(QC-failed)	0	0
% Singleton	0.0000	0.0000
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

Peak calling

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller MACS2

	overlap
Nt	0
N1	129754
Np	0
N optimal	129754
N conservative	129754
Optimal Set	rep1-pr
Conservative Set	rep1-pr
Rescue Ratio	0.0000
Self Consistency Ratio	1.0000
Reproducibility	pass

Overlapping peaks

N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Enrichment

Strand cross-correlation measures

Performed on subsampled reads (15M)

	rep1
Reads	15000000
Est. Fragment Len.	150
Corr. Est. Fragment Len.	0.1975
Phantom Peak	45
Corr. Phantom Peak	0.1868
Argmin. Corr.	1500
Min. Corr.	0.1796
NSC	1.0994
RSC	2.5123

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Fraction of reads in overlapping peaks

	rep1-pr
Fraction of Reads in Peak	0.4155

ppr: Overlapping peaks comparing pooled pseudo replicates
rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1
% genome enriched	0.1713
AUC	0.4950
CHANCE divergence	0.1560
Elbow Point	0.0000
JS Distance	0.7554
Synthetic AUC	0.5094
Synthetic Elbow Point	0.3168
Synthetic JS Distance	0.4527